The quake hit at 00:38 am local time (3.38am AEDT), the US Geological Survey said, and was centered around 300 kilometers northeast of Manado and 320 kilometers southeast of the Philippine city of General Santos.

The second quake struck in northern Japan just 30 minutes later, registering a preliminary magnitude of 6.0.

The Pacific Tsunami Warning Center said there was no tsunami threat from either quake.

Indonesia sits on the Pacific "Ring of Fire" where tectonic plates collide, causing frequent seismic and volcanic activity in the region.

A 6.9 quake struck in the Banda Sea in December sparked panic but no reports of damage or casualties.